Microbial Diversity in the Phyllosphere and Rhizosphere of an Apple Orchard Managed under Prolonged "Natural Farming" Practices.

Ying-Hong He,Akiko Kashiwagi,Tsutae Ito,Katsuhiko Yaginuma,Hideki Yamamoto,Charith Raj Adkar-Purushothama,Yuko Matsushita,Asuka Shirakawa,Ayumu Tatewaki,Seiya Tsushima,Misato Fujibayashi,Shuichi Sugiyama,Shingen Yamamoto,Tomoya Akahira,Teruo Sano

doi:10.3390/microorganisms9102056

Abstract

Microbial diversity in an apple orchard cultivated with natural farming practices for over 30 years was compared with conventionally farmed orchards to analyze differences in disease suppression. In this long-term naturally farmed orchard, major apple diseases were more severe than in conventional orchards but milder than in a short-term natural farming orchard. Among major fungal species in the phyllosphere, we found that Aureobasidium pullulans and Cryptococcus victoriae were significantly less abundant in long-term natural farming, while Cladosporium tenuissimum predominated. However, diversity of fungal species in the phyllosphere was not necessarily the main determinant in the disease suppression observed in natural farming; instead, the maintenance of a balanced, constant selection of fungal species under a suitable predominant species such as C. tenuissimum seemed to be the important factors. Analysis of bacteria in the phyllosphere revealed Pseudomonas graminis, a potential inducer of plant defenses, predominated in long-term natural farming in August. Rhizosphere metagenome analysis showed that Cordyceps and Arthrobotrys, fungal genera are known to include insect- or nematode-infecting species, were found only in long-term natural farming. Among soil bacteria, the genus Nitrospira was most abundant, and its level in long-term natural farming was more than double that in the conventionally farmed orchard.

Highlights

Microbial diversity, in both the phyllosphere and the rhizosphere, is thought to influence the formation and function of microbial environments in crops [1,2,3]
Soil bacterial community diversity in naturally farmed and conventionally farmed apple orchards was evaluated using 16S rRNA gene sequencing, and we found that many significant differences in the richness and evenness of operational taxonomic units were detectable at each taxonomic level (17)
Our results reveal the microbial species characteristic of the phyllosphere and rhizosphere of an apple orchard managed for a prolonged period under natural farming conditions

Summary

Introduction

In both the phyllosphere and the rhizosphere, is thought to influence the formation and function of microbial environments in crops [1,2,3]. Changes in the microbial community always lead to alterations of the host metagenomic environment, reflecting the ways in which pathogens attack and divert host functions and resources and Microorganisms 2021, 9, 2056. Predicting how changes in microbial diversity affect the functioning of an ecosystem requires an understanding of the complex interactions among microbial species at multiple levels [4]. The diversity of microbial inhabitants, especially those living in the phyllosphere or rhizosphere of agricultural crops, can be influenced by the natural environment (temperature, rainfall, soil type, mineral content) or by human activities, including cultural practices and pest-control management (chemical fertilizers, pesticides). Changes in microbial diversity are believed to play an important role in the health status and disease incidence among crops, either via competitive or antagonistic action toward pathogens or by stimulating the potential resistance and natural immunity of plants against them [7,8,9,10,11,12,13,14]

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